Crystal structure at 1.95 å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition

Dokurno, P.; Bates, Paul A.; Band, H.A.; Stewart, Lorna; Lally, John M.; Burchell, Joy; Taylor‐Papadimitriou, Joyce; Snary, David; Sternberg, Michael J.E.; Freemont, Paul S.

doi:10.1006/jmbi.1998.2209

Cited by 73 publications

(77 citation statements)

References 53 publications

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“…This is contrary to the trend seen to date, with the heavy chain CDRs being more involved in forming contacts in the case of most other peptide-Ab complexes (3). The amount of the buried surface area of the peptide is much higher than the average surface area buried in similar cases (464 -576 Å 2 ), observed until now (26). This is true also in case of the Ab (413-523 Å 2 ) (26).…”

Section: Discussioncontrasting

confidence: 56%

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Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-Antibody Recognition

Nair

Singh

Sahu

et al. 2000

The Journal of Immunology

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The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 Å2 for the peptide and 625 Å2 for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.

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Section: Discussioncontrasting

confidence: 56%

“…During refinement, the residue Ala51L consistently showed disallowed dihedral angles. Residues at this position have been observed in other Fab structures to possess disallowed dihedral angles (26 Fig. 2A) indicated that the density for the peptide was clearly defined.…”

Section: Pc283 Fab Structure and The Conformation Of The Bound Ps1 Pementioning

confidence: 64%

Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-Antibody Recognition

Nair

Singh

Sahu

et al. 2000

The Journal of Immunology

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“…The MUC1 peptide region containing the epitope (SAPDTR-PAP) of breast-tumor-specific Ab SM3 defined by crystal structure analysis (Protein Data Bank ID code 1SM3) (29) was docked onto the surface of the CD5 model by using the program AUTODOCK 3.05 (30). The procedures used for the docking can be found in Supporting Materials and Methods.…”

Section: Methodsmentioning

confidence: 99%

Dynamic force spectroscopy of parallel individual Mucin1–antibody bonds

Sulchek

Friddle

Langry

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

165

215

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We used atomic force microscopy to measure the binding forces between Mucin1 (MUC1) peptide and a single-chain variable fragment (scFv) antibody selected from a scFv library screened against MUC1. This binding interaction is central to the design of molecules used for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from nonspecific interactions by tethering the antibody and MUC1 molecules to the atomic force microscope tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the rupture events corresponding to different numbers of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for monovalent, bivalent, and trivalent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for monovalent and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in a parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.atomic force microscopy ͉ multivalency ͉ radioimmunmotherapy ͉ binding affinity I nteractions between biological molecules drive a vast variety of cellular processes and span a wide range of strength and complexity. Multivalent interactions where several binding units combine to produce superior binding strength play an important role in adaptive immune response (1) and intercellular adhesion (2), as well as in the mechanism of action of many pharmaceuticals (3). Clinical researchers have used multivalency as an affinity-enhancing approach (4, 5) in a variety of immunotherapies and imaging techniques to target specific tissues (6, 7).Linking several molecules into a large multivalent binding construct also creates bulky agents that exhibit reduced tissue penetration and have a higher probability of accumulation in liver (8). Therefore, a better understanding of the multivalent binding is necessary for the creation of optimized agents that balance binding efficiency and molecular size. Quantitative characterization of multivalent interactions is also important for understanding the basic biophysics of complex molecular systems.The last decade saw an explosion of interaction force measurement techniques that allowed researchers to measure and apply molecular level stresses (9-11). Atomic force microscopy (AFM) probes ligand-receptor interactions by simply pulling off the ligand from the receptor using external force (12). Kinetic approaches to the binding force measurements, such as dynamic force spectroscopy ...

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“…Despite their high profile generally as specific immunotherapeutic targets, there are no reported structures of a monoclonal antibody in complex with a glycopeptide. The only available structure is a glycopeptide-specific antibody in complex with its corresponding unglycosylated peptide (20), and a full characterization of the antibody recognition of clinically relevant glycopeptides is overdue.…”

mentioning

confidence: 99%

Antibody recognition of a unique tumor-specific glycopeptide antigen

Brooks

Schietinger

Borisova

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Aberrant glycosylation and the overexpression of certain carbohydrate moieties is a consistent feature of cancers, and tumorassociated oligosaccharides are actively investigated as targets for immunotherapy. One of the most common aberrations in glycosylation patterns is the presentation of a single O-linked N-acetylgalactosamine on a threonine or serine residue known as the "Tn antigen." Whereas the ubiquitous nature of Tn antigens on cancers has made them a natural focus of vaccine research, such carbohydrate moieties are not always tumor-specific and have been observed on embryonic and nonmalignant adult tissue. Here we report the structural basis of binding of a complex of a monoclonal antibody (237mAb) with a truly tumor-specific glycopeptide containing the Tn antigen. In contrast to glycopeptide-specific antibodies in complex with simple peptides, 237mAb does not recognize a conformational epitope induced in the peptide by sugar substitution. Instead, 237mAb uses a pocket coded by germ-line genes to completely envelope the carbohydrate moiety itself while interacting with the peptide moiety in a shallow groove. Thus, 237mAb achieves its striking tumor specificity, with no observed physiological cross-reactivity to the unglycosylated peptide or the free glycan, by a combination of multiple weak but specific interactions to both the peptide and to the glycan portions of the antigen.X-ray crystallography | affinity maturation | crystal structure

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Crystal structure at 1.95 å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition

Cited by 73 publications

References 53 publications

Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-Antibody Recognition

Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-Antibody Recognition

Dynamic force spectroscopy of parallel individual Mucin1–antibody bonds

Antibody recognition of a unique tumor-specific glycopeptide antigen

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